[gmx-developers] Coming on to help in GROMACS development

[Michael Shirts]

Before I head into the response, one thing I wanted to check is what
the release schedule is for the next versions of GROMACS, so I will
know how to time my contributions.  It's been hard to get any
information out on this subject :)

Back to the response:

> This depends a lot on the system I guess.
> For many system you do want to turn of the intramolecular non-bonded
> terms as the ensemble of the molecule would become very different
> in the vapor state, whereas a molecule without non-bonded interactions
> might have an ensemble closer to the solvated state.

Right, so this should be a configurable option.

> I guess that in put_in_list you would just have to check if both atoms
> are perturbed instead of only one in the pair.
> I have also made some changes put_in_list, especially for free-energy
> simulations

Yep, that's pretty much what needs to be done. 

> I accidentally put a question mark at the last line.
> I meant that I have implemented this and that it is in CVS.

Very good, I'll look over it.